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- PDB-6rg3: Crystal structure of human Carbonic anhydrase II in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6rg3
TitleCrystal structure of human Carbonic anhydrase II in complex with (R)-4-(2-benzylpiperazin-1-yl)benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase
Similarity search - Domain/homology
Chem-K1W / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.32 Å
AuthorsFerraroni, M. / Angeli, A. / Supuran, C.
CitationJournal: Bioorg.Chem. / Year: 2019
Title: Sulfonamides incorporating piperazine bioisosteres as potent human carbonic anhydrase I, II, IV and IX inhibitors.
Authors: Chiaramonte, N. / Bua, S. / Angeli, A. / Ferraroni, M. / Picchioni, I. / Bartolucci, G. / Braconi, L. / Dei, S. / Teodori, E. / Supuran, C.T. / Romanelli, M.N.
History
DepositionApr 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8064
Polymers29,2891
Non-polymers5173
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-7 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.364, 41.263, 71.918
Angle α, β, γ (deg.)90.000, 104.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K1W / 4-[(2~{R})-2-(phenylmethyl)piperazin-1-yl]carbonylbenzenesulfonamide


Mass: 359.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21N3O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1.5 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.827 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.32→41.09 Å / Num. obs: 56341 / % possible obs: 99.2 % / Redundancy: 3.346 % / Biso Wilson estimate: 22.209 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.055 / Χ2: 0.989 / Net I/σ(I): 12.39 / Num. measured all: 188539
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.32-1.413.3650.7741.24336431013199990.6430.92198.7
1.41-1.523.1620.3992.5629082934791970.8510.48198.4
1.52-1.673.4240.1845.6830792906889930.9630.21999.2
1.67-1.873.3090.09510.3226577805980320.9880.11499.7
1.87-2.153.4810.05518.2423775684268290.9960.06599.8
2.15-2.643.3730.04124.3720436608160590.9970.04899.6
2.64-3.723.4140.03133.1515721462546050.9980.03699.6
3.72-41.093.2410.02539.288513264626270.9990.0399.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4FIK

4fik


Resolution: 1.32→41.09 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.161 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0557 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.056
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 2719 4.8 %RANDOM
Rwork0.1771 ---
obs0.1781 53621 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.01 Å2 / Biso mean: 17.156 Å2 / Biso min: 9.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0.16 Å2
2--0.14 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.32→41.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 32 261 2358
Biso mean--17.95 28.91 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132215
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172010
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.6573019
X-RAY DIFFRACTIONr_angle_other_deg1.4621.6014713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2155277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93323.909110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55115372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.616157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02452
LS refinement shellResolution: 1.32→1.354 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5 200 -
Rwork0.508 3861 -
all-4061 -
obs--98.71 %

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